"When we decided to move forward with the national rollout of queso, we opted to replace chorizo on the line with queso, so chorizo is going away," Chris Arnold, spokesman for Chipotle, told CNBC via email. "While we really liked the chorizo (and many customers did too), the efficiency of our model has always been rooted in part, in doing just a few things so we can do them really well."

"Chorizo didn't sell as expected as it isn't a mainstream American consumer ingredient," Darren Tristano, a Technomic advisor, told CNBC via email. "Chorizo is a more authentic flavor and Chipotle serves the more 'Americanized' and pop marketplace. Queso is very popular and has likely had good results with consumers."

However, Chipotle could face some challenges with its queso moving forward. Not only is competition in the category intense, but many customers have not warmed up to the chain's version of queso dip.

In initial tests in Colorado and California, Chipotle's queso received tepid reviews, especially on Twitter. And that continued following its national rollout. Many said that the dip had a "grainy" texture while others applauded its smokey taste.

"A very negative reaction to the queso launch suggests [Chipotle] launched a product that is not meeting consumer expectations, and, as a result, missed a potentially significant opportunity to add queso as an incremental add-on," Karen Holthouse, a Goldman Sachs analyst, wrote in a research note Monday. "The consumer reaction on Twitter suggests few customers will become repeat users, and it could also limit any initial traffic bump around trial."

In comparison, California-based Del Taco recently launched its own queso blanco, which is smooth and creamy, like traditional queso, and has been getting rave reviews on Twitter since its launch.

"The impression is that Chipotle has no real strategy when it comes to menu innovation, it just seems to be grasping at straws in an attempt to come up with a winning product," Neil Saunders, managing director of GlobalData, told CNBC via email. "That both confuses customers and does no favors to the sales line."

Against a backdrop of sector-wide weakness, Chipotle shares were recently trading down more than 3.4 percent.